# HG changeset patch
# User rakesh4osdd
# Date 1624891162 0
# Node ID 9c7d056cac306f150a63ee069fc60bc124984d94
# Parent  c1a77856070c25cfe59fb74aa1ce90fe18f5c69c
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 2d3fa913c9fa9db73f4aa40799749f2247abaa80-dirty"

diff -r c1a77856070c -r 9c7d056cac30 clsi.csv
--- a/clsi.csv	Sat Jun 26 07:27:53 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-Antibiotics,Susceptible,Resistant,Intermediate
-Amikacin,≤ 16,≥ 64,32
-Tobramycin,≤ 4,≥ 16,8
-Gentamicin,≤ 4,≥ 16,8
-Netilmicin,≤ 8,≥ 32,16
-Imipenem,≤ 2,≥ 8,4
-Meropenem,≤ 2,≥ 8,4
-Doripenem,≤ 2,≥ 8,4
-Ciprofloxacin,≤ 1,≥ 4,2
-Levofloxacin,≤ 2,≥ 8,4
-Piperacillin/ tazobactam,≤ 16/4,≥ 128/4,32/4-64/4
-Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2,32/2-64/2
-Cefotaxime,≤ 8,≥ 64,16-32
-Ceftriaxone,≤ 8,≥ 64,16-32
-Ceftazidime,≤ 8,≥ 32,16
-Cefepime,≤ 8,≥ 32,16
-Trimethoprim/ sulfamethoxazole,≤ 2/38,≥ 4/76,-
-Ampicillin/ sulbactam,≤ 8/4,≥ 32/16,16/8
-Colistin,-,≥ 4,≤ 2
-Polymyxin B,-,≥ 4,≤ 2
-Tetracycline,≤ 4,≥ 16,8
-Doxycycline,≤ 4,≥ 16,8
-Minocycline,≤ 4,≥ 16,8
\ No newline at end of file
diff -r c1a77856070c -r 9c7d056cac30 input.csv
--- a/input.csv	Sat Jun 26 07:27:53 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-id,genome Ids,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,1,mg/L
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,2,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
-470,CP015483.1,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L
-470,470.7601,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7651,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7764,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.8071,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7405,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L
-470,470.7406,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L
-470,470.7407,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L
-470,470.7408,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
diff -r c1a77856070c -r 9c7d056cac30 test-data/input.csv
diff -r c1a77856070c -r 9c7d056cac30 tool_shed.sh
--- a/tool_shed.sh	Sat Jun 26 07:27:53 2021 +0000
+++ b/tool_shed.sh	Mon Jun 28 14:39:22 2021 +0000
@@ -1,4 +1,5 @@
 #!/bin/bash
 # After reviewing .shed.yml, this configuration file and relevant shed artifacts can be quickly linted using the following command.
 planemo shed_lint --tools
-planemo shed_create --shed_target toolshed 
+#planemo shed_create --shed_target toolshed 
+planemo shed_update --check_diff --shed_target toolshed